Starting phenix.real_space_refine on Fri Jul 3 17:59:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smk_40589/07_2026/8smk_40589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smk_40589/07_2026/8smk_40589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8smk_40589/07_2026/8smk_40589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smk_40589/07_2026/8smk_40589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8smk_40589/07_2026/8smk_40589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smk_40589/07_2026/8smk_40589.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.387 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 82 5.16 5 C 9712 2.51 5 N 2556 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15298 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4348 Classifications: {'peptide': 555} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 520} Chain breaks: 10 Chain: "B" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1653 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 207} Chain: "C" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1644 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Restraints were copied for chains: D, E, F Time building chain proxies: 5.14, per 1000 atoms: 0.34 Number of scatterers: 15298 At special positions: 0 Unit cell: (139.445, 181.195, 105.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 82 16.00 O 2940 8.00 N 2556 7.00 C 9712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.16 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.16 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 719.6 milliseconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 44 sheets defined 15.3% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 557 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 192 through 195 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 320 through 330 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 471 through 474 Processing helix chain 'D' and resid 494 through 507 Processing helix chain 'D' and resid 526 through 531 Processing helix chain 'D' and resid 532 through 557 Processing helix chain 'D' and resid 560 through 562 No H-bonds generated for 'chain 'D' and resid 560 through 562' Processing helix chain 'D' and resid 611 through 621 Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 7.226A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.312A pdb=" N VAL A 283 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP A 273 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 285 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 removed outlier: 8.740A pdb=" N GLY A 390 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL A 392 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 367 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 335 removed outlier: 7.049A pdb=" N GLN A 306 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR A 335 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 308 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB2, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AB3, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.712A pdb=" N ILE B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.146A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.146A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 115 through 119 removed outlier: 4.991A pdb=" N SER C 132 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU C 182 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL C 134 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU C 180 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU C 136 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 178 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN C 138 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 176 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 155 removed outlier: 4.069A pdb=" N ALA C 194 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 8 removed outlier: 7.226A pdb=" N ILE D 7 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR D 15 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR D 111 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 17 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 113 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS D 19 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 115 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 20 removed outlier: 6.750A pdb=" N THR D 15 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR D 111 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 17 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 113 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS D 19 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 115 " --> pdb=" O CYS D 19 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL D 213 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.312A pdb=" N VAL D 283 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP D 273 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 285 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU D 199 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 297 through 298 removed outlier: 8.740A pdb=" N GLY D 390 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL D 392 " --> pdb=" O PRO D 365 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 367 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 333 through 335 removed outlier: 7.048A pdb=" N GLN D 306 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR D 335 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 308 " --> pdb=" O THR D 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AD3, first strand: chain 'D' and resid 416 through 418 Processing sheet with id=AD4, first strand: chain 'D' and resid 476 through 480 Processing sheet with id=AD5, first strand: chain 'D' and resid 571 through 573 Processing sheet with id=AD6, first strand: chain 'D' and resid 590 through 592 Processing sheet with id=AD7, first strand: chain 'D' and resid 605 through 606 Processing sheet with id=AD8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.712A pdb=" N ILE E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 128 through 132 removed outlier: 6.146A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 139 through 140 removed outlier: 6.146A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 159 through 162 Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.991A pdb=" N SER F 132 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU F 182 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL F 134 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU F 180 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU F 136 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER F 178 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN F 138 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU F 176 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 154 through 155 removed outlier: 4.068A pdb=" N ALA F 194 " --> pdb=" O LYS F 150 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2690 1.32 - 1.44: 4017 1.44 - 1.56: 8807 1.56 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 15630 Sorted by residual: bond pdb=" N PRO F 8 " pdb=" CD PRO F 8 " ideal model delta sigma weight residual 1.474 1.405 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" N PRO C 8 " pdb=" CD PRO C 8 " ideal model delta sigma weight residual 1.474 1.405 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" N PRO A 480 " pdb=" CD PRO A 480 " ideal model delta sigma weight residual 1.473 1.411 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" N PRO D 480 " pdb=" CD PRO D 480 " ideal model delta sigma weight residual 1.473 1.411 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" N PRO D 436 " pdb=" CD PRO D 436 " ideal model delta sigma weight residual 1.473 1.413 0.060 1.40e-02 5.10e+03 1.87e+01 ... (remaining 15625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 17590 1.78 - 3.56: 3111 3.56 - 5.34: 453 5.34 - 7.12: 46 7.12 - 8.90: 12 Bond angle restraints: 21212 Sorted by residual: angle pdb=" N ALA A 119 " pdb=" CA ALA A 119 " pdb=" C ALA A 119 " ideal model delta sigma weight residual 111.74 120.64 -8.90 1.35e+00 5.49e-01 4.34e+01 angle pdb=" N ALA D 119 " pdb=" CA ALA D 119 " pdb=" C ALA D 119 " ideal model delta sigma weight residual 111.74 120.64 -8.90 1.35e+00 5.49e-01 4.34e+01 angle pdb=" C PRO F 142 " pdb=" N ARG F 143 " pdb=" CA ARG F 143 " ideal model delta sigma weight residual 120.28 128.11 -7.83 1.34e+00 5.57e-01 3.41e+01 angle pdb=" C PRO C 142 " pdb=" N ARG C 143 " pdb=" CA ARG C 143 " ideal model delta sigma weight residual 120.28 128.08 -7.80 1.34e+00 5.57e-01 3.38e+01 angle pdb=" C PHE D 261 " pdb=" N PRO D 262 " pdb=" CA PRO D 262 " ideal model delta sigma weight residual 119.56 125.13 -5.57 1.02e+00 9.61e-01 2.99e+01 ... (remaining 21207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 9046 16.99 - 33.98: 222 33.98 - 50.97: 50 50.97 - 67.95: 50 67.95 - 84.94: 18 Dihedral angle restraints: 9386 sinusoidal: 3662 harmonic: 5724 Sorted by residual: dihedral pdb=" C ARG A 123 " pdb=" N ARG A 123 " pdb=" CA ARG A 123 " pdb=" CB ARG A 123 " ideal model delta harmonic sigma weight residual -122.60 -131.66 9.06 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" C ARG D 123 " pdb=" N ARG D 123 " pdb=" CA ARG D 123 " pdb=" CB ARG D 123 " ideal model delta harmonic sigma weight residual -122.60 -131.66 9.06 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" CA SER A 413 " pdb=" C SER A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 9383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1747 0.064 - 0.129: 472 0.129 - 0.193: 181 0.193 - 0.258: 8 0.258 - 0.322: 2 Chirality restraints: 2410 Sorted by residual: chirality pdb=" CA ARG D 123 " pdb=" N ARG D 123 " pdb=" C ARG D 123 " pdb=" CB ARG D 123 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ARG A 123 " pdb=" N ARG A 123 " pdb=" C ARG A 123 " pdb=" CB ARG A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ALA D 119 " pdb=" N ALA D 119 " pdb=" C ALA D 119 " pdb=" CB ALA D 119 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2407 not shown) Planarity restraints: 2704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 105 " 0.107 2.00e-02 2.50e+03 5.40e-02 5.83e+01 pdb=" CG TYR E 105 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR E 105 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR E 105 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR E 105 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR E 105 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 105 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 105 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " -0.107 2.00e-02 2.50e+03 5.40e-02 5.82e+01 pdb=" CG TYR B 105 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 94 " -0.045 2.00e-02 2.50e+03 3.22e-02 2.08e+01 pdb=" CG TYR B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR B 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 94 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 94 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 94 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR B 94 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR B 94 " -0.062 2.00e-02 2.50e+03 ... (remaining 2701 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 65 2.62 - 3.19: 12539 3.19 - 3.76: 22358 3.76 - 4.33: 32705 4.33 - 4.90: 53252 Nonbonded interactions: 120919 Sorted by model distance: nonbonded pdb=" OD1 ASP A 168 " pdb="CA CA A 704 " model vdw 2.054 3.250 nonbonded pdb=" OD1 ASP D 168 " pdb="CA CA D 704 " model vdw 2.054 3.250 nonbonded pdb=" OD2 ASP D 157 " pdb="CA CA D 702 " model vdw 2.096 3.250 nonbonded pdb=" OD2 ASP A 157 " pdb="CA CA A 702 " model vdw 2.096 3.250 nonbonded pdb=" OD1 ASP D 155 " pdb="CA CA D 702 " model vdw 2.115 3.250 ... (remaining 120914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.170 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.127 15634 Z= 0.746 Angle : 1.377 8.897 21220 Z= 0.958 Chirality : 0.064 0.322 2410 Planarity : 0.008 0.083 2704 Dihedral : 11.016 84.943 5678 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 1930 helix: 0.55 (0.36), residues: 180 sheet: 1.12 (0.19), residues: 690 loop : 0.86 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 427 TYR 0.107 0.003 TYR E 105 PHE 0.039 0.003 PHE D 487 TRP 0.049 0.006 TRP A 466 HIS 0.002 0.000 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.01136 / 0.74 (15630) covalent geometry : angle 1.37648 / 0.96 (21212) SS BOND : bond 0.08971 / 5.08 ( 4) SS BOND : angle 2.72888 / 1.70 ( 8) hydrogen bonds : bond 0.19103 / 13.32 ( 592) hydrogen bonds : angle 7.94756 / 5.55 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8038 (mt) cc_final: 0.7801 (pt) REVERT: A 184 THR cc_start: 0.8525 (m) cc_final: 0.8032 (p) REVERT: A 188 LYS cc_start: 0.7566 (tttt) cc_final: 0.6967 (tttt) REVERT: A 196 ASN cc_start: 0.7803 (m-40) cc_final: 0.7225 (p0) REVERT: A 244 LYS cc_start: 0.8542 (tptt) cc_final: 0.7769 (tptt) REVERT: A 502 GLN cc_start: 0.7073 (tp40) cc_final: 0.6773 (mm110) REVERT: A 527 LYS cc_start: 0.6746 (pttt) cc_final: 0.6389 (mtpp) REVERT: B 77 ASN cc_start: 0.8409 (t0) cc_final: 0.7883 (t0) REVERT: B 186 LEU cc_start: 0.8419 (pp) cc_final: 0.8133 (pp) REVERT: C 61 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7195 (mtp180) REVERT: C 77 SER cc_start: 0.7998 (m) cc_final: 0.7243 (t) REVERT: C 79 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7326 (mp10) REVERT: C 83 PHE cc_start: 0.8410 (m-80) cc_final: 0.8184 (m-80) REVERT: C 177 SER cc_start: 0.8305 (t) cc_final: 0.7670 (p) REVERT: C 178 SER cc_start: 0.8087 (t) cc_final: 0.7767 (p) REVERT: D 24 LEU cc_start: 0.8043 (mt) cc_final: 0.7802 (pt) REVERT: D 184 THR cc_start: 0.8520 (m) cc_final: 0.8025 (p) REVERT: D 188 LYS cc_start: 0.7562 (tttt) cc_final: 0.6953 (tttt) REVERT: D 196 ASN cc_start: 0.7799 (m-40) cc_final: 0.7226 (p0) REVERT: D 244 LYS cc_start: 0.8539 (tptt) cc_final: 0.7774 (tptt) REVERT: D 502 GLN cc_start: 0.7075 (tp40) cc_final: 0.6778 (mm110) REVERT: D 527 LYS cc_start: 0.6747 (pttt) cc_final: 0.6390 (mtpp) REVERT: E 77 ASN cc_start: 0.8400 (t0) cc_final: 0.7874 (t0) REVERT: E 186 LEU cc_start: 0.8411 (pp) cc_final: 0.8127 (pp) REVERT: F 61 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7200 (mtp180) REVERT: F 77 SER cc_start: 0.7996 (m) cc_final: 0.7237 (t) REVERT: F 79 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7316 (mp10) REVERT: F 83 PHE cc_start: 0.8411 (m-80) cc_final: 0.8188 (m-80) REVERT: F 177 SER cc_start: 0.8311 (t) cc_final: 0.7878 (p) REVERT: F 178 SER cc_start: 0.8078 (t) cc_final: 0.7861 (p) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1379 time to fit residues: 90.5282 Evaluate side-chains 270 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0970 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 471 HIS ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 471 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.178486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131326 restraints weight = 22841.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133351 restraints weight = 11451.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135645 restraints weight = 7829.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136334 restraints weight = 6200.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136631 restraints weight = 5782.852| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15634 Z= 0.137 Angle : 0.586 6.779 21220 Z= 0.311 Chirality : 0.045 0.143 2410 Planarity : 0.005 0.055 2704 Dihedral : 4.420 18.179 2100 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.62 % Allowed : 7.57 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1930 helix: 1.87 (0.38), residues: 182 sheet: 1.34 (0.19), residues: 762 loop : 1.01 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 484 TYR 0.018 0.002 TYR F 141 PHE 0.016 0.001 PHE A 407 TRP 0.011 0.001 TRP D 141 HIS 0.005 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15630) covalent geometry : angle 0.58602 / 0.31 (21212) SS BOND : bond 0.00291 / 0.17 ( 4) SS BOND : angle 0.81464 / 0.44 ( 8) hydrogen bonds : bond 0.04109 / 2.83 ( 592) hydrogen bonds : angle 5.35964 / 3.70 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8397 (m) REVERT: A 188 LYS cc_start: 0.7639 (tttt) cc_final: 0.7243 (tttt) REVERT: A 193 PHE cc_start: 0.9088 (t80) cc_final: 0.8737 (t80) REVERT: A 196 ASN cc_start: 0.8049 (m-40) cc_final: 0.7469 (p0) REVERT: A 244 LYS cc_start: 0.8497 (tptt) cc_final: 0.7501 (tptt) REVERT: A 247 MET cc_start: 0.8035 (tpt) cc_final: 0.7828 (tpt) REVERT: A 276 ASN cc_start: 0.8393 (t0) cc_final: 0.7508 (t0) REVERT: A 352 MET cc_start: 0.7481 (mtt) cc_final: 0.7226 (mtt) REVERT: A 407 PHE cc_start: 0.7604 (m-10) cc_final: 0.7294 (m-80) REVERT: A 474 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7870 (mt-10) REVERT: A 527 LYS cc_start: 0.7055 (pttt) cc_final: 0.6434 (mtpp) REVERT: A 554 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8443 (mtpt) REVERT: B 77 ASN cc_start: 0.8524 (t0) cc_final: 0.8175 (t0) REVERT: C 22 THR cc_start: 0.8603 (p) cc_final: 0.8363 (t) REVERT: C 140 PHE cc_start: 0.8302 (p90) cc_final: 0.7809 (p90) REVERT: C 167 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 45 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8390 (m) REVERT: D 188 LYS cc_start: 0.7641 (tttt) cc_final: 0.7248 (tttt) REVERT: D 193 PHE cc_start: 0.9089 (t80) cc_final: 0.8738 (t80) REVERT: D 196 ASN cc_start: 0.8053 (m-40) cc_final: 0.7484 (p0) REVERT: D 244 LYS cc_start: 0.8498 (tptt) cc_final: 0.7504 (tptt) REVERT: D 247 MET cc_start: 0.8031 (tpt) cc_final: 0.7826 (tpt) REVERT: D 276 ASN cc_start: 0.8390 (t0) cc_final: 0.7505 (t0) REVERT: D 352 MET cc_start: 0.7476 (mtt) cc_final: 0.7220 (mtt) REVERT: D 407 PHE cc_start: 0.7603 (m-10) cc_final: 0.7291 (m-80) REVERT: D 474 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7875 (mt-10) REVERT: D 527 LYS cc_start: 0.7058 (pttt) cc_final: 0.6436 (mtpp) REVERT: D 554 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8444 (mtpt) REVERT: E 77 ASN cc_start: 0.8524 (t0) cc_final: 0.8175 (t0) REVERT: F 22 THR cc_start: 0.8598 (p) cc_final: 0.8357 (t) REVERT: F 140 PHE cc_start: 0.8303 (p90) cc_final: 0.7786 (p90) REVERT: F 167 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7759 (tm-30) REVERT: F 177 SER cc_start: 0.8173 (t) cc_final: 0.7837 (p) REVERT: F 178 SER cc_start: 0.8261 (t) cc_final: 0.8046 (p) outliers start: 28 outliers final: 14 residues processed: 308 average time/residue: 0.1400 time to fit residues: 62.6932 Evaluate side-chains 242 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 554 LYS Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 6 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 59 optimal weight: 0.0050 chunk 181 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 0.0060 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121991 restraints weight = 23491.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125952 restraints weight = 12759.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128544 restraints weight = 8775.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130230 restraints weight = 6965.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131243 restraints weight = 6008.171| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15634 Z= 0.148 Angle : 0.564 9.050 21220 Z= 0.291 Chirality : 0.044 0.143 2410 Planarity : 0.005 0.046 2704 Dihedral : 4.208 17.646 2100 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.20 % Allowed : 9.83 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1930 helix: 1.66 (0.38), residues: 196 sheet: 1.30 (0.19), residues: 760 loop : 0.73 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 102 TYR 0.022 0.002 TYR E 153 PHE 0.014 0.001 PHE D 583 TRP 0.011 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (15630) covalent geometry : angle 0.56390 / 0.29 (21212) SS BOND : bond 0.00142 / 0.09 ( 4) SS BOND : angle 0.74255 / 0.41 ( 8) hydrogen bonds : bond 0.03604 / 2.48 ( 592) hydrogen bonds : angle 4.96678 / 3.42 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8237 (ttp) cc_final: 0.7989 (ttp) REVERT: A 193 PHE cc_start: 0.9113 (t80) cc_final: 0.8696 (t80) REVERT: A 196 ASN cc_start: 0.8179 (m-40) cc_final: 0.7550 (p0) REVERT: A 352 MET cc_start: 0.7698 (mtt) cc_final: 0.7447 (mtt) REVERT: A 464 SER cc_start: 0.9234 (p) cc_final: 0.8926 (t) REVERT: A 527 LYS cc_start: 0.7140 (pttt) cc_final: 0.6560 (mtpp) REVERT: A 554 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: B 77 ASN cc_start: 0.8515 (t0) cc_final: 0.8187 (t0) REVERT: C 22 THR cc_start: 0.8580 (p) cc_final: 0.8342 (t) REVERT: D 164 MET cc_start: 0.8238 (ttp) cc_final: 0.7989 (ttp) REVERT: D 193 PHE cc_start: 0.9114 (t80) cc_final: 0.8698 (t80) REVERT: D 196 ASN cc_start: 0.8177 (m-40) cc_final: 0.7551 (p0) REVERT: D 352 MET cc_start: 0.7696 (mtt) cc_final: 0.7430 (mtt) REVERT: D 464 SER cc_start: 0.9226 (p) cc_final: 0.8911 (t) REVERT: D 527 LYS cc_start: 0.7136 (pttt) cc_final: 0.6561 (mtpp) REVERT: D 554 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8595 (mtpt) REVERT: E 77 ASN cc_start: 0.8515 (t0) cc_final: 0.8187 (t0) REVERT: F 22 THR cc_start: 0.8582 (p) cc_final: 0.8342 (t) outliers start: 38 outliers final: 29 residues processed: 263 average time/residue: 0.1446 time to fit residues: 54.7860 Evaluate side-chains 232 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 554 LYS Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 0.0050 chunk 44 optimal weight: 2.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.171770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120197 restraints weight = 23345.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124155 restraints weight = 12657.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126716 restraints weight = 8685.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128372 restraints weight = 6881.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129348 restraints weight = 5946.072| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15634 Z= 0.147 Angle : 0.551 7.928 21220 Z= 0.284 Chirality : 0.044 0.189 2410 Planarity : 0.005 0.043 2704 Dihedral : 4.141 17.225 2100 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.66 % Allowed : 9.77 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1930 helix: 1.26 (0.38), residues: 204 sheet: 1.40 (0.18), residues: 792 loop : 0.58 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.015 0.001 TYR F 49 PHE 0.013 0.001 PHE A 582 TRP 0.009 0.001 TRP A 659 HIS 0.004 0.001 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15630) covalent geometry : angle 0.55106 / 0.28 (21212) SS BOND : bond 0.00155 / 0.10 ( 4) SS BOND : angle 0.63116 / 0.35 ( 8) hydrogen bonds : bond 0.03348 / 2.32 ( 592) hydrogen bonds : angle 4.77630 / 3.31 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9084 (t80) cc_final: 0.8658 (t80) REVERT: A 196 ASN cc_start: 0.8224 (m-40) cc_final: 0.7655 (p0) REVERT: A 464 SER cc_start: 0.9224 (p) cc_final: 0.8887 (t) REVERT: A 527 LYS cc_start: 0.7330 (pttt) cc_final: 0.6777 (mtpp) REVERT: B 77 ASN cc_start: 0.8536 (t0) cc_final: 0.8217 (t0) REVERT: C 22 THR cc_start: 0.8571 (p) cc_final: 0.8275 (t) REVERT: D 193 PHE cc_start: 0.9084 (t80) cc_final: 0.8658 (t80) REVERT: D 196 ASN cc_start: 0.8226 (m-40) cc_final: 0.7659 (p0) REVERT: D 464 SER cc_start: 0.9251 (p) cc_final: 0.8902 (t) REVERT: D 527 LYS cc_start: 0.7316 (pttt) cc_final: 0.6771 (mtpp) REVERT: E 77 ASN cc_start: 0.8535 (t0) cc_final: 0.8216 (t0) REVERT: F 22 THR cc_start: 0.8570 (p) cc_final: 0.8272 (t) outliers start: 46 outliers final: 27 residues processed: 236 average time/residue: 0.1409 time to fit residues: 48.3674 Evaluate side-chains 229 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN D 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122083 restraints weight = 23095.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125586 restraints weight = 11591.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126365 restraints weight = 7796.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126873 restraints weight = 6981.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126944 restraints weight = 6276.421| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15634 Z= 0.168 Angle : 0.565 8.482 21220 Z= 0.291 Chirality : 0.044 0.185 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.248 17.276 2100 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.37 % Allowed : 10.40 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1930 helix: 1.42 (0.38), residues: 202 sheet: 1.35 (0.18), residues: 786 loop : 0.44 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 66 TYR 0.016 0.001 TYR F 49 PHE 0.014 0.001 PHE D 582 TRP 0.010 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (15630) covalent geometry : angle 0.56522 / 0.29 (21212) SS BOND : bond 0.00104 / 0.07 ( 4) SS BOND : angle 0.63097 / 0.35 ( 8) hydrogen bonds : bond 0.03397 / 2.35 ( 592) hydrogen bonds : angle 4.77423 / 3.31 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8260 (m-40) cc_final: 0.7735 (p0) REVERT: A 464 SER cc_start: 0.9236 (p) cc_final: 0.8902 (t) REVERT: A 527 LYS cc_start: 0.7335 (pttt) cc_final: 0.6733 (mtpp) REVERT: A 576 PHE cc_start: 0.7366 (m-80) cc_final: 0.7058 (t80) REVERT: B 77 ASN cc_start: 0.8576 (t0) cc_final: 0.7975 (t0) REVERT: C 22 THR cc_start: 0.8613 (p) cc_final: 0.8360 (t) REVERT: C 42 LYS cc_start: 0.8864 (mmtp) cc_final: 0.8529 (mttp) REVERT: D 196 ASN cc_start: 0.8260 (m-40) cc_final: 0.7739 (p0) REVERT: D 464 SER cc_start: 0.9249 (p) cc_final: 0.8926 (t) REVERT: D 527 LYS cc_start: 0.7334 (pttt) cc_final: 0.6732 (mtpp) REVERT: D 576 PHE cc_start: 0.7369 (m-80) cc_final: 0.7060 (t80) REVERT: E 77 ASN cc_start: 0.8576 (t0) cc_final: 0.7983 (t0) REVERT: F 22 THR cc_start: 0.8616 (p) cc_final: 0.8364 (t) REVERT: F 42 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8528 (mttp) outliers start: 41 outliers final: 31 residues processed: 240 average time/residue: 0.1420 time to fit residues: 48.9891 Evaluate side-chains 231 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 30.0000 chunk 168 optimal weight: 0.6980 chunk 188 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122998 restraints weight = 23171.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125089 restraints weight = 11857.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126648 restraints weight = 8319.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127218 restraints weight = 7142.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127340 restraints weight = 6498.100| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15634 Z= 0.136 Angle : 0.546 8.284 21220 Z= 0.277 Chirality : 0.044 0.184 2410 Planarity : 0.005 0.045 2704 Dihedral : 4.112 17.174 2100 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.97 % Allowed : 11.50 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 1930 helix: 1.62 (0.38), residues: 202 sheet: 1.40 (0.18), residues: 778 loop : 0.42 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.015 0.001 TYR C 49 PHE 0.016 0.001 PHE D 40 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15630) covalent geometry : angle 0.54558 / 0.28 (21212) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.58922 / 0.33 ( 8) hydrogen bonds : bond 0.03214 / 2.23 ( 592) hydrogen bonds : angle 4.66475 / 3.23 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8966 (t80) cc_final: 0.8549 (t80) REVERT: A 196 ASN cc_start: 0.8182 (m-40) cc_final: 0.7638 (p0) REVERT: A 464 SER cc_start: 0.9249 (p) cc_final: 0.8934 (t) REVERT: A 527 LYS cc_start: 0.7286 (pttt) cc_final: 0.6713 (mtpp) REVERT: A 576 PHE cc_start: 0.7419 (m-80) cc_final: 0.7076 (t80) REVERT: B 77 ASN cc_start: 0.8568 (t0) cc_final: 0.8035 (t0) REVERT: C 22 THR cc_start: 0.8637 (p) cc_final: 0.8396 (t) REVERT: C 42 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8491 (mttp) REVERT: D 193 PHE cc_start: 0.8968 (t80) cc_final: 0.8549 (t80) REVERT: D 196 ASN cc_start: 0.8187 (m-40) cc_final: 0.7641 (p0) REVERT: D 464 SER cc_start: 0.9252 (p) cc_final: 0.8929 (t) REVERT: D 527 LYS cc_start: 0.7281 (pttt) cc_final: 0.6709 (mtpp) REVERT: D 576 PHE cc_start: 0.7414 (m-80) cc_final: 0.7072 (t80) REVERT: E 77 ASN cc_start: 0.8553 (t0) cc_final: 0.8026 (t0) REVERT: F 22 THR cc_start: 0.8637 (p) cc_final: 0.8393 (t) REVERT: F 42 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8489 (mttp) outliers start: 34 outliers final: 26 residues processed: 235 average time/residue: 0.1359 time to fit residues: 46.5244 Evaluate side-chains 231 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 157 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.173788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127251 restraints weight = 22850.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129476 restraints weight = 11743.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131215 restraints weight = 7965.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131631 restraints weight = 6833.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132112 restraints weight = 6173.603| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15634 Z= 0.102 Angle : 0.535 8.319 21220 Z= 0.267 Chirality : 0.043 0.176 2410 Planarity : 0.004 0.045 2704 Dihedral : 3.870 15.833 2100 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.20 % Allowed : 12.02 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1930 helix: 1.80 (0.38), residues: 202 sheet: 1.52 (0.18), residues: 782 loop : 0.45 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.012 0.001 TYR F 49 PHE 0.008 0.001 PHE F 97 TRP 0.008 0.001 TRP E 162 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (15630) covalent geometry : angle 0.53509 / 0.27 (21212) SS BOND : bond 0.00067 / 0.04 ( 4) SS BOND : angle 0.49117 / 0.28 ( 8) hydrogen bonds : bond 0.02899 / 2.00 ( 592) hydrogen bonds : angle 4.47201 / 3.10 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8893 (t80) cc_final: 0.8295 (t80) REVERT: A 196 ASN cc_start: 0.8170 (m-40) cc_final: 0.7733 (p0) REVERT: A 207 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: A 215 GLN cc_start: 0.7942 (tt0) cc_final: 0.7685 (tt0) REVERT: A 464 SER cc_start: 0.9259 (p) cc_final: 0.8961 (t) REVERT: A 527 LYS cc_start: 0.7288 (pttt) cc_final: 0.6807 (mtpp) REVERT: A 576 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7030 (t80) REVERT: B 77 ASN cc_start: 0.8518 (t0) cc_final: 0.7862 (t0) REVERT: B 89 GLU cc_start: 0.8878 (pm20) cc_final: 0.8660 (pm20) REVERT: C 22 THR cc_start: 0.8635 (p) cc_final: 0.8319 (t) REVERT: C 42 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8503 (mttp) REVERT: D 193 PHE cc_start: 0.8893 (t80) cc_final: 0.8295 (t80) REVERT: D 196 ASN cc_start: 0.8169 (m-40) cc_final: 0.7733 (p0) REVERT: D 207 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: D 215 GLN cc_start: 0.7936 (tt0) cc_final: 0.7687 (tt0) REVERT: D 464 SER cc_start: 0.9264 (p) cc_final: 0.8949 (t) REVERT: D 527 LYS cc_start: 0.7289 (pttt) cc_final: 0.6808 (mtpp) REVERT: D 576 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7028 (t80) REVERT: E 77 ASN cc_start: 0.8512 (t0) cc_final: 0.7877 (t0) REVERT: F 22 THR cc_start: 0.8633 (p) cc_final: 0.8320 (t) REVERT: F 42 LYS cc_start: 0.8762 (mmtp) cc_final: 0.8506 (mttp) outliers start: 38 outliers final: 22 residues processed: 242 average time/residue: 0.1366 time to fit residues: 48.2455 Evaluate side-chains 230 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.171124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123241 restraints weight = 23246.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126995 restraints weight = 11734.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127788 restraints weight = 7704.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128323 restraints weight = 6888.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128458 restraints weight = 6240.819| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15634 Z= 0.134 Angle : 0.553 8.315 21220 Z= 0.280 Chirality : 0.043 0.182 2410 Planarity : 0.005 0.047 2704 Dihedral : 4.001 16.678 2100 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.02 % Allowed : 12.37 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.20), residues: 1930 helix: 1.97 (0.39), residues: 202 sheet: 1.46 (0.18), residues: 796 loop : 0.41 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.015 0.001 TYR C 49 PHE 0.012 0.001 PHE D 583 TRP 0.009 0.001 TRP D 141 HIS 0.004 0.001 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (15630) covalent geometry : angle 0.55256 / 0.28 (21212) SS BOND : bond 0.00086 / 0.06 ( 4) SS BOND : angle 0.54538 / 0.30 ( 8) hydrogen bonds : bond 0.03026 / 2.10 ( 592) hydrogen bonds : angle 4.51548 / 3.13 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8942 (t80) cc_final: 0.8412 (t80) REVERT: A 196 ASN cc_start: 0.8262 (m-40) cc_final: 0.7813 (p0) REVERT: A 464 SER cc_start: 0.9271 (p) cc_final: 0.8990 (t) REVERT: A 527 LYS cc_start: 0.7391 (pttt) cc_final: 0.6880 (mtpp) REVERT: A 576 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 77 ASN cc_start: 0.8626 (t0) cc_final: 0.8033 (t0) REVERT: B 89 GLU cc_start: 0.8937 (pm20) cc_final: 0.8723 (pm20) REVERT: C 22 THR cc_start: 0.8623 (p) cc_final: 0.8308 (t) REVERT: C 42 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8567 (mttp) REVERT: D 193 PHE cc_start: 0.8945 (t80) cc_final: 0.8413 (t80) REVERT: D 196 ASN cc_start: 0.8259 (m-40) cc_final: 0.7811 (p0) REVERT: D 464 SER cc_start: 0.9266 (p) cc_final: 0.8983 (t) REVERT: D 527 LYS cc_start: 0.7357 (pttt) cc_final: 0.6850 (mtpp) REVERT: D 576 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7038 (t80) REVERT: E 77 ASN cc_start: 0.8588 (t0) cc_final: 0.8042 (t0) REVERT: F 22 THR cc_start: 0.8626 (p) cc_final: 0.8312 (t) REVERT: F 42 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8563 (mttp) outliers start: 35 outliers final: 25 residues processed: 232 average time/residue: 0.1357 time to fit residues: 46.3818 Evaluate side-chains 231 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 80 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 148 optimal weight: 0.0870 chunk 192 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.171764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125193 restraints weight = 22910.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128794 restraints weight = 11396.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129560 restraints weight = 7627.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129959 restraints weight = 6670.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130129 restraints weight = 6136.878| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15634 Z= 0.126 Angle : 0.557 8.390 21220 Z= 0.281 Chirality : 0.043 0.180 2410 Planarity : 0.004 0.046 2704 Dihedral : 3.972 16.550 2100 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.50 % Allowed : 12.95 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.20), residues: 1930 helix: 1.87 (0.39), residues: 204 sheet: 1.52 (0.19), residues: 778 loop : 0.41 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 24 TYR 0.014 0.001 TYR C 49 PHE 0.017 0.001 PHE D 40 TRP 0.009 0.001 TRP B 162 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (15630) covalent geometry : angle 0.55717 / 0.28 (21212) SS BOND : bond 0.00052 / 0.03 ( 4) SS BOND : angle 0.49756 / 0.28 ( 8) hydrogen bonds : bond 0.02963 / 2.05 ( 592) hydrogen bonds : angle 4.46324 / 3.09 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8929 (t80) cc_final: 0.8453 (t80) REVERT: A 196 ASN cc_start: 0.8236 (m-40) cc_final: 0.7844 (p0) REVERT: A 464 SER cc_start: 0.9267 (p) cc_final: 0.9009 (t) REVERT: A 527 LYS cc_start: 0.7388 (pttt) cc_final: 0.6911 (mtpp) REVERT: A 576 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 62 ASP cc_start: 0.8137 (m-30) cc_final: 0.7875 (m-30) REVERT: B 77 ASN cc_start: 0.8557 (t0) cc_final: 0.8098 (t0) REVERT: B 89 GLU cc_start: 0.8943 (pm20) cc_final: 0.8727 (pm20) REVERT: C 22 THR cc_start: 0.8612 (p) cc_final: 0.8308 (t) REVERT: C 42 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8529 (mttp) REVERT: D 193 PHE cc_start: 0.8929 (t80) cc_final: 0.8452 (t80) REVERT: D 196 ASN cc_start: 0.8236 (m-40) cc_final: 0.7842 (p0) REVERT: D 321 LYS cc_start: 0.7179 (mmtt) cc_final: 0.6812 (mmtt) REVERT: D 464 SER cc_start: 0.9256 (p) cc_final: 0.8977 (t) REVERT: D 527 LYS cc_start: 0.7379 (pttt) cc_final: 0.6881 (mtpp) REVERT: D 576 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7006 (t80) REVERT: E 62 ASP cc_start: 0.8134 (m-30) cc_final: 0.7837 (m-30) REVERT: E 77 ASN cc_start: 0.8520 (t0) cc_final: 0.8076 (t0) REVERT: F 22 THR cc_start: 0.8613 (p) cc_final: 0.8311 (t) REVERT: F 42 LYS cc_start: 0.8786 (mmtp) cc_final: 0.8533 (mttp) outliers start: 26 outliers final: 23 residues processed: 227 average time/residue: 0.1288 time to fit residues: 43.0557 Evaluate side-chains 219 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 110 optimal weight: 0.0570 chunk 107 optimal weight: 0.0070 chunk 145 optimal weight: 0.0470 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.0370 chunk 27 optimal weight: 0.8980 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.175032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130594 restraints weight = 23154.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131966 restraints weight = 11399.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134249 restraints weight = 7805.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134455 restraints weight = 6108.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134674 restraints weight = 5917.287| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15634 Z= 0.093 Angle : 0.537 8.505 21220 Z= 0.268 Chirality : 0.043 0.168 2410 Planarity : 0.004 0.045 2704 Dihedral : 3.741 15.388 2100 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.50 % Allowed : 13.29 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.20), residues: 1930 helix: 2.00 (0.39), residues: 204 sheet: 1.58 (0.19), residues: 796 loop : 0.49 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.009 0.001 TYR F 49 PHE 0.007 0.001 PHE A 291 TRP 0.007 0.001 TRP A 659 HIS 0.003 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (15630) covalent geometry : angle 0.53706 / 0.27 (21212) SS BOND : bond 0.00082 / 0.05 ( 4) SS BOND : angle 0.48250 / 0.27 ( 8) hydrogen bonds : bond 0.02653 / 1.82 ( 592) hydrogen bonds : angle 4.28156 / 2.96 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8175 (m-40) cc_final: 0.7811 (p0) REVERT: A 464 SER cc_start: 0.9268 (p) cc_final: 0.8999 (t) REVERT: A 527 LYS cc_start: 0.7339 (pttt) cc_final: 0.6890 (mtpp) REVERT: A 576 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6999 (t80) REVERT: B 77 ASN cc_start: 0.8406 (t0) cc_final: 0.8002 (t0) REVERT: C 45 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8052 (ttpp) REVERT: D 196 ASN cc_start: 0.8181 (m-40) cc_final: 0.7807 (p0) REVERT: D 321 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6771 (mmtt) REVERT: D 464 SER cc_start: 0.9249 (p) cc_final: 0.8973 (t) REVERT: D 527 LYS cc_start: 0.7342 (pttt) cc_final: 0.6894 (mtpp) REVERT: D 576 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6990 (t80) REVERT: E 77 ASN cc_start: 0.8409 (t0) cc_final: 0.8006 (t0) REVERT: F 45 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8047 (ttpp) outliers start: 26 outliers final: 20 residues processed: 233 average time/residue: 0.1350 time to fit residues: 46.5018 Evaluate side-chains 222 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.171676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125627 restraints weight = 22971.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127894 restraints weight = 11631.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129451 restraints weight = 7875.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129884 restraints weight = 6813.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129897 restraints weight = 6211.347| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15634 Z= 0.130 Angle : 0.563 8.592 21220 Z= 0.283 Chirality : 0.044 0.179 2410 Planarity : 0.005 0.045 2704 Dihedral : 3.889 16.770 2100 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.39 % Allowed : 14.05 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1930 helix: 2.05 (0.39), residues: 204 sheet: 1.59 (0.19), residues: 760 loop : 0.49 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 218 TYR 0.013 0.001 TYR C 49 PHE 0.010 0.001 PHE A 583 TRP 0.010 0.001 TRP D 141 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (15630) covalent geometry : angle 0.56344 / 0.28 (21212) SS BOND : bond 0.00047 / 0.03 ( 4) SS BOND : angle 0.45542 / 0.25 ( 8) hydrogen bonds : bond 0.02914 / 2.02 ( 592) hydrogen bonds : angle 4.35966 / 3.01 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.61 seconds wall clock time: 53 minutes 19.66 seconds (3199.66 seconds total)